Frequently Asked Questions

Peapod Bio is a contract research organization (CRO) based in Chicago, Illinois, specializing in biochemical assay development and high-throughput screening (HTS) for small molecule and peptide drug discovery. We partner with pharmaceutical companies, biotechs, and academic institutions to advance early-stage drug discovery programs.

Our core expertise and unique solution is our label-free MALDI mass spectrometry-based platform powered by Polymeric Enrichment Array (PEA) technology, enabling faster, higher-confidence data that complements our traditional assay readouts such as HTRF, AlphaLISA, luminescence, fluorescence, fluorescence polarizaiton, and our world-class small molecule library.

Peapod Bio supports a broad range of enzyme classes and protein targets, including kinases, phosphatases, methyltransferases, acetyltransferases, deubiquitinases, ubiquitin ligases, proteases, polymerases, nucleases, glycosyltransferases, and more. We also support non-enzymatic assay development to identify small molecule and peptide binders for protein-protein interaction and induced proximity.studies.

We work with diverse analytes, including small molecules, peptides, oligonucleotides, proteins, and antibodies, and support drug modalities including enzyme inhibitors and activators, molecular glue and other proximity-inducing compounds for targeted protein degradation and other proximity mechanisms.

Several factors distinguish Peapod Bio from traditional CROs: our proprietary label-free MALDI-MS platform powered by PEAs delivers decision-driving data at unprecedented turnaround times. We offer a flexible approach to tailor solutions to your specific program needs and project goals. We view our team as an extension of your lab, acting as a true partner in discovery. Clients also cite our responsive communication and hands-on scientific collaboration as differentiators.

Label-free assays measure the native biochemical activity of your target directly without attaching fluorescent dyes, radioactive isotopes, or other reporter molecules to your compound or protein. Label-free assays eliminate artifacts such as spurious interactions between labels and proteins and optical interference that increase false positive results They also avoid the costly and time-consuming synthesis of labeled probes and reduce the need for multiple orthogonal assays to validate label-generated data.

The result is cleaner, more trustworthy data with fewer false positives, generated faster and with greater confidence to support go/no-go decisions.

Peapod Bio uses the rapifleX MALDI Pharmapulse (MPP) system from Bruker Daltonics, a state-of-the-art high-throughput MALDI mass spectrometer specifically engineered for drug discovery workflows. Combined with our proprietary Polymeric Enrichment Arrays (PEAs), this platform enables direct, label-free measurement of biochemical activity and binding interactions at ultra high-throughput speeds. Importantly, the PEAs enable the optimization of assays without any limitations in buffers, including salts and detergents, eliminating the ion suppression challenge with traditional MALDI MS.

PEAs are Peapod Bio’s proprietary sample preparation technology that rapidly purifies analytes of interest prior to MALDI-MS analysis. Most label-free mass spectrometry approaches require extensive sample cleanup steps that limit throughput and constrain assay conditions. PEAs eliminate those bottlenecks, allowing for clean, interpretable results without compromising assay design or reagent flexibility.

PEAs are compatible with any buffer component, including salts, detergents, and cell lysates, giving scientists full freedom to optimize their assay conditions without the limitations imposed by traditional MS platforms.

Yes. While label-free MALDI-MS with PEAs is our signature technology, we offer a full suite of orthogonal optical assay formats, including fluorescence, luminescence, HTRF, AlphaLISA, and fluorescence polarization, for situations where those methodologies are a best fit to achieve your drug discovery goals.

ASMS is a screening method used to identify small molecule and peptide binders to a target protein or nucleic acid. ASMS is ideal when you want to find hits for targets that lack a robust enzyme activity or when you want to cast a wide net for any molecule that binds, regardless of mechanism.

It’s particularly powerful for:

• Challenging targets such as RNA: Reliably detects binders to traditionally undruggable proteins and nucleic acid structures
• Proximity inducers and molecular glues: Specifically optimized for small molecule binding and informing on ternary complex formation
• Validation of virtual screening and DNA encoded library (DEL) hits: Serves as a high-throughput follow-up to validate predicted binders and confirm the direct interaction rather than functional activity between a small molecule and its target.

Traditional ASMS requires a multi-step sample preparation process, such as size exclusion chromatography followed by denaturation chromatography that are slow. To overcome the throughput limitation, traditional ASMS workflows often compress small molecule libraries with hundreds of compounds per well. The caveat is that high compression promotes compound misbehavior and increases false positive results. As more compounds are added, the compound concentration decreases, and weaker, yet still tractable hits, will be missed.

Peapod Bio’s PEA-powered ASMS platform is the fastest commercial ASMS workflow and eliminates all chromatography steps. Target-small molecule complexes are isolated using the PEAs and the small molecule (or peptide) binders are dissociated directly by the MALDI laser. The ultra high-throughput speed of the rapifleX MALDI PharmaPulse enables us to test only 12 compounds per pool. This strategy accelerates the screen while drastically reducing compound misbehavior, generating higher-quality, decision-driving data while improving the detection of weak binders, which is especially important for difficult targets where even modest affinity compounds can serve as valuable starting points.

Yes. our ASMS platform is designed to work with virtually any target, including RNA independent of size and sequence. It also has unique solutions for ternary complex screening, making it a strong fit for molecular glue, proteolysis targeting chimeras (PROTACs), and other chemical inducers of proximity programs.

Peapod Bio develops tailored biochemical assays for enzyme activity and binding interactions (e.g., protein-protein interactions, and proximity-inducing mechanisms). Our assay development solutions include elucidating reaction mechanisms, defining kinetic parameters, profiling potency and selectivity, characterizing diverse enzyme activities, and building assays optimized for high-throughput screening.

We support enzyme classes spanning kinases, phosphatases, methyltransferases, acetyltransferases, deubiquitinases, ubiquitin ligases, proteases, polymerases, glycosyltransferases, and many more, and a variety of assay readouts to increase the likelihood of success for your program.

Peapod Bio develops assays in days rather than in weeks or months. We have identified opportunities to accelerate the discovery process, including skipping tedious sample preparation steps and leveraging deep expertise in MALDI MS, to enable rapid workflows without compromising on data quality. Biochemical experiments aim to measure enzyme linearity, KM determination, DMSO tolerance, and uniformity prior to testing compounds.

Yes! This is one of our core strengths. We have expertise in challenging target classes including multi-component complexes, nucleic acids (e.g., RNA as a target for binding), membrane-bound proteins in nanodiscs or peptidiscs, intrinsically disordered proteins (IDPs) and more!

High-throughput screening with Peapod Bio may include primary screening, hit confirmation, and concentration response curves (CRCs) to validate screening results. We work with you throughout the process, handling all compound management, sourcing compounds when necessary, and providing data in a format that integrates with your internal databases.

In addition, we use the same high-throughput approach to run routine assays to measure IC50s or EC50s (for ASMS assays). Our rapid data delivery ensures that companies accelerate DMTA cycles whether for iterative chemistry or feeding AI/ML models.

We maintain an in-house collection of 200,000 small molecules curated for drug-like properties, with an average compound purity greater than 95%. The library is available as single compounds for biochemical HTS and as pools of 12 compounds for ASMS campaigns.

The library is diverse and designed to maximize chemical space coverage to improve your odds of finding a quality hit from day one. Through a partnership with Enamine, Peapod Bio has access to 5 million compounds for hit expansion and powder stocks for potency and selectivity profiling.

Yes. Our platform is fully compatible with externally supplied compound libraries. You can screen your proprietary collection, an independent library, or combine it with our in-house library, whichever approach best fits your program strategy.